2D1V | pdb_00002d1v

Crystal structure of DNA-binding domain of Bacillus subtilis YycF

PDB DOI: https://doi.org/10.2210/pdb2D1V/pdb

Classification: TRANSCRIPTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-09-01 Released: 2006-09-12
Deposition Author(s): Okajima, T., Okada, A., Watanabe, T., Yamamoto, K., Tanizawa, K., Utsumi, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.232 (Depositor), 0.231 (DCC)
R-Value Work:
0.228 (Depositor), 0.229 (DCC)
R-Value Observed:
0.229 (Depositor)

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This is version 1.4 of the entry. See complete history.

Literature

Response regulator YycF essential for bacterial growth: X-ray crystal structure of the DNA-binding domain and its PhoB-like DNA recognition motif

Okajima, T., Doi, A., Okada, A., Gotoh, Y., Tanizawa, K., Utsumi, R.

(2008) FEBS Lett 582: 3434-3438

PubMed: 18789936 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2008.09.007
Primary Citation Related Structures:
2D1V

PubMed Abstract:
A response regulator YycF and its cognate sensor kinase YycG constitute the two-component signal transduction system essential for growth of Gram-positive bacteria with a low GC content. We have determined the X-ray crystal structure of the effector domain of Bacillus subtilis YycF involved in DNA binding. The structure, containing a winged helix-turn-helix motif, was found to be very similar to that of the response regulator PhoB from Escherichia coli. Specific binding of YycF to the PhoB-regulated alkaline phosphatase promoter was also demonstrated.

Organizational Affiliation

Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan. tokajima@sanken.osaka-u.ac.jp

Macromolecule Content

Total Structure Weight: 12.81 kDa
Atom Count: 901
Modeled Residue Count: 103
Deposited Residue Count: 108
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein yycF	A	108	Bacillus subtilis	Mutation(s): 0 Gene Names: yycF
UniProt
Find proteins for P37478 (Bacillus subtilis (strain 168)) Explore P37478 Go to UniProtKB: P37478
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P37478
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.232 (Depositor), 0.231 (DCC)
R-Value Work: 0.228 (Depositor), 0.229 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.754	α = 90
b = 65.584	β = 90
c = 79.07	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-09-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-09-12
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-03-13
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.